Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2-NAPHTHYL-GUANINE ADDUCT IN ANTI ORIENTATION DOI:10.2210/pdb2w8l/pdb   NDB ID: 2W8L

2W8L   Display Files  close FASTA Sequence PDB File PDB File (Header) mmCIF File mmCIF File (Header) PDBML/XML File PDBML/XML File (Header)   Download Files  close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly (gz) (A+S)   Share this Page  close Facebook Twitter LinkedIn Email Link this Page

ENTRY 2W8L SUPERSEDES 2V4T Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Transferase/dna Structure Weight: 51549.90 Molecule: DNA POLYMERASE IV Polymer: 1 Type: protein Length: 358 Chains: A EC#: 2.7.7.7    Details: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS Organism Sulfolobus solfataricus P2 Gene Names dbh dpo4 SSO2448 UniProtKB:   Protein Feature View | Search PDB | Q97W02     Molecule: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3' Polymer: 2 Type: dna Length: 14 Chains: P Details: 14 BASE PRIMER DNA 5'-GGG GGA AGG ATT CC-3' Molecule: 5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3' Polymer: 3 Type: dna Length: 18 Chains: T Details: 18 BASE TEMPLATE DNA 5'-TCA C(NPG)G AAT CCT TCC CCC-3'     Source Hide Polymer: 1 Scientific Name: Sulfolobus solfataricus   Taxonomy   Expression System: Escherichia coli   Polymer: 2 Scientific Name: Synthetic construct   Taxonomy     Polymer: 3 Scientific Name: Synthetic construct   Taxonomy         Related PDB Entries Hide Identifier Details 1JX4  CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE  1JXL  CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE  1N48  Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC LESION  1N56  Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC LESION  1RYR  REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION  1RYS  REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION  1S0M  CRYSTAL STRUCTURE OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCTIN A TERNARY COMPLEX WITH A DNA POLYMERASE  1S0N  SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT  1S0O  SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT  1S10  SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT  1S97  DPO4 WITH GT MISMATCH  1S9F  DPO WITH AT MATCHED  2AGO  FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS  2AGP  FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS  2AGQ  FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS  2ASD  OXOG-MODIFIED INSERTION TERNARY COMPLEX  2ASJ  OXOG-MODIFIED PREINSERTION BINARY COMPLEX  2ASL  OXOG-MODIFIED POSTINSERTION BINARY COMPLEX  2ATL  UNMODIFIED INSERTION TERNARY COMPLEX  2AU0  UNMODIFIED PREINSERTION BINARY COMPLEX  2BQ3  DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE  2BQR  DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE  2BQU  DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE  2BR0  DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE  2C22  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2C28  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2C2D  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2C2E  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2C2R  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2J6S  TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.  2J6T  TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.  2J6U  TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DGTP.  2JEF  THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOTIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING  2JEG  THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING  2JEI  THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING  2JEJ  THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING  2UVR  CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS  2UVU  CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS  2UVV  CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS  2UVW  CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS  2V4Q  POST-INSERTION COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH M1DG CONTAINING TEMPLATE DNA  2V4R  NON-PRODUCTIVE COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE CYTOSINE  2V9W  COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND  2VA2  COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND  2VA3  COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND  2W8K  Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2-NAPHTHYL-GUANINE ADDUCT IN SYN ORIENTATION      Ligand Chemical Component Hide Identifier Formula Name Interactions DGT Search  Download  C10 H16 N5 O13 P3 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE   Ligand Explorer MG Search  Download  Mg MAGNESIUM ION   Ligand Explorer     External Ligand Annotations Hide Identifier   Binding Affinity (Sequence Identity %) DGT Search  Download  N/A in BindingDB N/A in BindingMoad Kd: 29000 nM - data from PDBbind       Modified Residues Hide Identifier Formula Parent Type DOC Search  C9 H14 N3 O6 P DC dnaLinking N2G Search  C21 H22 N5 O7 P nonPolymer     External Domain Annotations Hide Pfam Classification: 3 Domains - data from Pfam   GO Terms: 12 Terms - data from GO      Structural Biology Knowledgebase Data Hide   Nucleic Acid Database Hide View the NDB ID associated with this structure: 2W8L     Data in orange boxes are gathered from external resources (when available). 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Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors and generated by PISA (software) Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Eoff, R.L.,  Zhang, H.,  Egli, M.,  Guengerich, F.P. Deposition:   2009-01-16 Release:   2009-01-27 Last Modified (REVDAT):   2010-08-25 Previous versions:  2V4T     Revision History    Hide Mouse over text for details 2011-07-13 Version format compliance     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors EDS   Resolution[Å]:   3.00 R-Value: 0.226 (obs.) R-Free: 0.282 Space Group: P 21 21 2 Unit Cell:   Length [Å] Angles [°] a = 95.92 α = 90.00  b = 103.83 β = 90.00  c = 52.49 γ = 90.00      Molecule of the Month Hide Thymine Dimers